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Correct the reverse-feeding implication in chloronitrobenzene degradation #1738
Description
CommunityMech:000181; PMID10049867. Preserve all three nodes, both directions, chemically supported upstream transformation, downstream intermediate degradation and reported conditional mineralization. Rhodococcus Intermediate Degradation is currently typed as CROSS_FEEDING from Rhodococcus to Pseudomonas, although the cited transformation runs from Pseudomonas-derived intermediates to Rhodococcus degradation. Represent the downstream process collectively with canonical participants, without inventing reverse metabolite provision. Remove categorical SYNTROPHY from the mineralization endpoint; preserve the reported result and added-carbon condition. Abstract-only limits must not be presented as proof that detailed controls were absent. Close only after protected-main merge.
Dedup:1006 all-state issue titles/bodies searched by IDs, PMIDs, names and broad substrate/taxon aliases. All nine matching bodies read; none is this graph repair. Explicitly read529/573/605 for general source/panel/membership scope.49 local matching files found with ignored/hidden included; .git/docs/site/references_cache excluded, relevant caches separately inspected. Comments and PRs not exhaustive. Self-adversarial review, not independent approval.
Activity
realmarcin commentedon Oct 7, 2026
Precommit adversarial correction: the actual SYNTROPHY enum explicitly does not require obligacy. The naphthalene transfer/circuit nodes retain the authors qualified SYNTROPHY model. The chloronitro endpoint remains untyped because pathway completion alone does not establish product-removal feedback, not because obligacy is unproven. Original histories and the initial 816-test validation are preserved as superseded; two correction histories and a schema-contract test have been added. Fresh full validation is in progress. No new causal direction or Edison job. Keep repairs open until protected-main merge.
realmarcin commentedon Oct 7, 2026
Addressed in #1743 at c12b1dc; exact-head self-review: #1743 (review). 817 passed in 280.29s (0:04:40); postcommit docs-current passed. Decisions and actual output digests committed. Not independent approval; close only after protected-main merge. Metadata1742remains unfinished.